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1 <tool id="PHYLO_classification" name="Output classifications" version="2.1.0">
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2 <description>in tabular format</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6
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6 <requirements>
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7 <requirement type="package">yapp_env</requirement>
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8 </requirements>
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9 <stdio>
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10 <expand macro="basic_errors"/>
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11 </stdio>
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12 <version_command>echo "pplacer $(pplacer --version)"</version_command>
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13 <command interpreter="bash">
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14 classification-wrapper.sh ${config}
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15 </command>
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16 <inputs>
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17 <param name="split_map" type="data" format="csv" label="Read-to-specimen map"/>
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18 <param name="label_map" type="data" format="csv" label="Specimen-to-label map"/>
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19 <param name="class_db" type="data" format="sqlite3" label="Placement database"/>
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20 <param name="want_rank" type="select" label="Desired classification rank">
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21 <option value="species" selected="true">Species</option>
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22 <option value="genus">Genus</option>
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23 <option value="family">Family</option>
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24 <option value="order">Order</option>
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25 <option value="class">Class</option>
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26 <option value="phylum">Phylum</option>
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27 </param>
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28 </inputs>
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29 <outputs>
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30 <data name="by_taxon" format="csv" label="By-taxon classification"/>
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31 <data name="by_specimen" format="csv" label="By-specimen classification"/>
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32 <data name="tallies_wide" format="csv" label="Tallies-wide classification"/>
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33 </outputs>
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34 <configfiles>
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35 <configfile name="config">
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36 SPLIT_MAP="${split_map}"
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37 LABEL_MAP="${label_map}"
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38 CLASS_DB="${class_db}"
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39 WANT_RANK="${want_rank}"
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40
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41 BY_TAXON="${by_taxon}"
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42 BY_SPECIMEN="${by_specimen}"
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43 TALLIES_WIDE="${tallies_wide}"
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44 </configfile>
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45 </configfiles>
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46 <!-- The contents of the help tag is parsed as reStructuredText. Please see
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47 help-template.rst for examples of commonly-used sections in other Galaxy
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48 tools. -->
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49 <help>
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50
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51 .. class:: infomark
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52
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53 **What it does**
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54
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55 This tool outputs the classifications made by ``pplacer`` to a tabular format
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56 appropriate for use with R.
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57
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58 -----
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59
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60 **Example**
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61
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62 The classifications are simply done by containment. Say clade A of the
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63 reference tree is the smallest such that contains a given placement. The most
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64 specific classification for that read will be the lowest common ancestor of the
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65 taxonomic classifications for the leaves of A. If the desired classification is
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66 more specific than that, then we get a disconnect between the desired and the
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67 actual classification. For example, if we try to classify at the species level
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68 and the clade LCA is a genus, then we will get a genus name. If there is
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69 uncertainty in read placement, then there is uncertainty in classification.
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70
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71 For example, here is a classification list made for one read using the tabular
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72 output. The columns are as follows: read name, attempted rank for
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73 classification, actual rank for classification, taxonomic identifier, and
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74 confidence. You can see that in this example, there is some uncertainty at and
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75 below species, but only one classification at the genus level::
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76
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77 GLKT0ZE01CQ2BU root root 1 1
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78 GLKT0ZE01CQ2BU below_root below_root 131567 1
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79 GLKT0ZE01CQ2BU superkingdom superkingdom 2 1
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80 GLKT0ZE01CQ2BU below_superkingdom superkingdom 2 1
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81 GLKT0ZE01CQ2BU below_below_superkingdom superkingdom 2 1
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82 GLKT0ZE01CQ2BU superphylum superkingdom 2 1
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83 GLKT0ZE01CQ2BU phylum phylum 1239 1
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84 GLKT0ZE01CQ2BU subphylum phylum 1239 1
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85 GLKT0ZE01CQ2BU class class 186801 1
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86 GLKT0ZE01CQ2BU subclass class 186801 1
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87 GLKT0ZE01CQ2BU order order 186802 1
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88 GLKT0ZE01CQ2BU below_order order 186802 1
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89 GLKT0ZE01CQ2BU below_below_order order 186802 1
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90 GLKT0ZE01CQ2BU suborder order 186802 1
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91 GLKT0ZE01CQ2BU family family 186804 1
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92 GLKT0ZE01CQ2BU below_family family 186804 1
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93 GLKT0ZE01CQ2BU genus genus 1257 1
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94 GLKT0ZE01CQ2BU species_group genus 1257 1
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95 GLKT0ZE01CQ2BU species_subgroup genus 1257 1
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96 GLKT0ZE01CQ2BU species genus 1257 0.0732247
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97 GLKT0ZE01CQ2BU species species 1261 0.853561
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98 GLKT0ZE01CQ2BU species species 341694 0.073214
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99 GLKT0ZE01CQ2BU below_species genus 1257 0.0732247
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100 GLKT0ZE01CQ2BU below_species species 1261 0.853561
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101 GLKT0ZE01CQ2BU below_species species 341694 0.073214
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102
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103 </help>
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6
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104 <citations>
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105 <expand macro="cite_pplacer"/>
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106 </citations>
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107 </tool>
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